Reign of Unicron
by Neodammarung the Destroyer
Summary: The Cybertronian Civil War had raged for aeons without end, yet after six years of relative peace, the Autobots and their allies believed that perhaps they had seen the last of their ruthless foe...but they were wrong. Sequel to Same Side by Era Yachi.
1. Prelude

Transformers 3

Reign of Unicron

It began on Cybertron, this war without end. All attempts to end it have cost us dearly. We sacrificed everything to stop the cycle of destruction; our friends, our home…our very survival as a species, yet nothing seemed to break our enemy's determination. Then, six years ago, the Decepticons went silent, vanishing without a trace. We thought it might finally be over.

But we were wrong…


	2. Part I Prologue

Part I: Signs and Portents

It is said, that in the final days of the universe that all living things suffered from bad dreams. It was worst on the planet that was to be the crux of the events to come, the world known to its people as 'Earth'. On the continent called 'North America', in the nation known as the United States, the populace did gather in a prideful festival to celebrate their independence and power.

Every person there had dreamt of the terrible things to come, of the dark fate that awaited them…but they forgot, because they must. They forgot the images of the fire and the war and the insanity that was drawing ever closer because the waking world was still full of joy and light. They all forgot…except one.


	3. Part I Chapter 1: Executioner's Song

Chapter 1: Executioner's Song

…_These are the things that you shall see: what is, what was and what shall be…fire and darkness…remorse is the pain of sin, and he feels none…nothing shall stay his wrath…for seven billion years, a secret in the silence…one by one, the stars will go out…every species, young and old, far and near, shall feel his return…it is inevitable…a great hand reaching out of the stars…the whole universe will perish in his shadow…they shall look up and shout 'Spare us'…and he will whisper…'No'…his hour draws nigh…the circle of the seventeen holds the key…the prophecy unfolds…he is awake…and they shall worship him…your last days are here…the cords of destiny wind together….so it was written, so it shall be…the Hellgate shall open…and Darkness shall fall…_

Sam Witwicky jerked awake with a grunt at the sudden pain in his ribs. He quickly and guiltily looked around the classroom. No one seemed to have noticed his odd behavior, luckily…except for his roommate Eli, who was sitting on his right and who glared at him briefly before returning to taking notes.

Sam felt embarrassed. He had never fallen asleep in any of his classes, not even ancient history, which he took only because a requirement of the job he was aiming for when he finally got his last degrees. He had seen many dedicated students lose focus five minutes into a lecture on ancient history. In Sam's mind, falling asleep during a lecture was something only a slacker would do, which made him feel even worse for doing it. The fact that his sudden narcolepsy wasn't his fault didn't help the ease his shame one bit.

A few years back, Sam had come into contact with the last remaining piece of an ancient alien artifact called the Allspark, a cube whose full purpose he had never really figured out. That simple touch with the tiny sliver of metal left over from the cube's destruction had infused his brain with an awesome amount of information that had immediately begun to unroll itself in his head, causing him to suffer from what could only be called 'informational seizures'.

When they stuck, alien calligraphy filled his vision and he felt a sort of itch, not a physical feeling but a mental compulsion, one that seemed to take control of his hands and place his body on autopilot. When he eventually regained control, he would find that he had filled every available surface with alien text. It was disconcerting at first, and had led to more than a few embarrassing situations that he would much rather forget, but in the end he had managed to find a way to prepare for them by carrying writing materials everywhere he went.

These 'informational trances' had been taking a lot out of him recently due to their unexplainably increasing frequency of occurrence. However, the endless stream of gibberish his brain seemed to be unstoppably spitting out onto paper these days only ever hurt his wrist, which was nothing compared to the sleep he was losing over the dreams, or more appropriately, the nightmares clouding his head. The images and dark words brought to him in his sleep seemed to scar his very soul, leaving the taste of blood and the little-kid fear of being watched by some indescribable evil with him whenever he woke up.

He did his best to remain awake while Professor Wilson while he continued to drone on about the various geological features found on the surface Mars, a subject that would probably have bored anyone who wasn't interested to tears. But Sam had developed a high tolerance for such things and besides, he needed this class if he was going to achieve the qualifications necessary for his dream job.

"-the Tharsis region of Mars is probably the most famous region in scientific circles. It is a vast volcanic plain that dominates the western hemisphere of the planet and which houses the largest volcanic land features in the solar system. The primary features everyone focuses on are Olympus Mons and its sister volcanoes Pavonis, Arsia and Ascreaus Mons, also known collectively as the Tharsis Montes," Professor Wilson said, pacing up and down in front of the chalkboards that lined the front of the classroom.

After a brief pause, in which he made his way over to a table next to his speaking podium in order to get some water and allow his students to catch up with their notes, he continued. His face was beginning to shine with a thin veil of sweat, his face having already turned a shade of red due to the July heat and the lack of adequate air conditioning in this old building.

Sam's mind drifted away again as the lecture continued, like a herd of sheep without a shepherd…he shook himself awake again before that train of thought could drag him back into unconsciousness and came back just in time to hear the professor switch topics to another major geological feature.

"low-lying volcanic landmark has an area comparable to the entire United States, but it only reaches six-point-eight kilometers in height at its maximum elevation, meaning it is often overlooked by the casual observer-,". Even before the professor had finished the sentence, Sam's mind was wandering against his will.

As his teacher continued to ramble on about the features of the Tharsis region, he began to feel a sensation that required some examination. It felt like the auto-writing compulsion, but was somehow different, less like a compulsion and more like an ominous vibe. The hairs on the back of his neck rose.

The lecture continued for another forty minutes with Sam fighting the dark sensation all the way. At about five 'o' clock, the professor reached the end of his rope. He stopped and collected some papers from his podium, then tried to get more water from the empty pitcher on the table next to the podium. Frustrated when nothing came out, he turned to face his students, his features now resembling an apple in color and sheen. He ruffled through the papers and then finally appeared to find what he was looking for.

"That'll be all for today. Just to remind you, your papers on the volcanic dynamics of Io are due on Tuesday. Also, expect a test on the features of Neptune's moons Thursday. Class dismissed." He said tersely. Then he headed for his desk while his students collected their belongings and shuffled to the door with Eli and Sam among them.

As they made their way into the hall, Sam turned to Eli.

"Thanks for getting my attention. I'm sorry about that-,"he managed to say before Eli cut him off.

"Sam, go back to the apartment, get some sleep. I've been watching you and those dark circles under your eyes have been getting bigger all week. You need to rest!" he said, irritation lacing every syllable. Sam tried to muster an answer.

"I can't. I've got a date with Mikaela at six," He managed to get out. Eli rolled his eyes.

"You're no good to her, much less anyone half-dead. Look, I'll drive you back-,"his friend tried to say, but Sam waved his hand dismissively.

"I'm FINE. Look, I'll get to bed early and take tomorrow off if you're so hot and bothered about this." Sam said. They walked on in silence for a while until Eli put his hand on Sam's shoulder.

"Sam…I've been meaning to talk to you about your love life…," he said, which made Sam stumble with surprise. Eli was not usually the kind of guy who discussed personal relationships out in the open.

"Um, Eli, could we talk about this later?" he said uncomfortably. But his friend pressed on.

"Dude, you're lucky Mikaela's stuck with you this long. Any other girl would've thought you were afraid to commit and run off. Hell, she even moved to the East Coast just to be with you! You need to have the wedding, preferably before she loses patience." He said. Sam squirmed.

"Eli, I really don't want to talk about this…" he mumbled. But when Eli was determined, nothing could stop him.

"Have you picked out the flowers? Who's going to be the best man? Honestly, Sam, you can't count on an engagement ring to hold you both together." His roommate said, earning him an odd look from Sam. In Sam's eyes, Eli was a little young to be considering marriage. Sure, he was twenty-one and all and he _did_ have a girlfriend whom Sam had met several times, but still, it was mind boggling. Then again, you probably had to grow up really fast when you had a mother dying of AIDS.

Eli Wallace had replaced Leo Spitz as Sam's roommate only a few years earlier. Sam still looked like he was eighteen, and Eli had actually been eighteen, but had Sam's mind beat on oh-so-many levels. The kid had already achieved two PhDs by age eighteen and was working on his Masters when they had agreed to share an apartment. Sam was amazed he hadn't been recruited by the Stargate Program already. It had proved to be a mutually beneficial arrangement. Eli was far less annoying than Leo had been and a lot more helpful. They were practically co-writing each other's theses.

"Um…Eli, look, you need to understand, what Mikaela and I have is…well it's complicated. I know I should be preparing, I really do, but…-,"Sam was at a loss at what to say next. He couldn't go on because if he told Eli that the affairs top-secret government organization dealing with the protection of the entire planet had a way of spilling over into his personal life, he would be doing nothing but damage to his reputation with his roommate. Besides, Eli wouldn't believe him in any case and it wasn't the sort of information he was allowed to share.

Sam had been engaged to Mikaela Banes for upwards of four years now, possibly the longest courtship-period in the history of marital affairs. They both loved each other, and Sam hadn't been afraid when he had given her the engagement ring. Sam wasn't afraid of marriage or commitment either. He _was_ afraid that the endless information trapped in his head, along with all the problems brought on by its being where it was, did scare him. On more than one occasion, psychopathic, power-hungry aliens had used people close to him to try and get a hold of the maelstrom of information in his brain.

True, it had been several years since the last incident in which someone had made a grab for him via his loved ones, but that fear remained and every time he thought he had worked up enough courage to finally go ahead with the ceremony, an image would flash through his head of himself standing over her coffin because of how he was a such a magnet for insanity and the image of the wedding party in his head would evaporate.

He eventually realized he had stopped walking and Eli was looking at him expectantly, waiting for him to finish his explanation. He sighed.

"It's just that I've got a lot going on right now. I'm trying to build a life for me and her before I go through with the ceremony." He finished. It sounded a bit lame when it came out. Eli's expression of disgust only confirmed his fears.

"Dude, you're pushing the envelope. Your procrastination isn't going to get you anywhere-,"his roommate began.

"Listen, I'll get back to you about the homework after my date and then I'll get some sleep. Happy?" he said. Eli snorted, and then turned away.

"Whatever, man." He said. Then he stalked off down the hall. Sam felt like a tool. He wanted to tell Eli the real reason, he really did. The kid deserved to know. He would probably handle it a lot better than Leo had done when he had first found out too.

In fact, Sam wouldn't mind working by him at the SGC…but that wasn't for him to decide. He couldn't say anything because then he'd be arrested and stuck in a cell in Area 51. Maybe the next time he saw his 'government friends', he'd ask them about it.

Sam made his way out to the parking garage two blocks down from the school building and made his way up four flights of stairs. For any other sleep derived person, driving one's self home was a bad idea…but most sleep deprived people didn't have a car that was actually an alien robot in disguise. Sam walked up to the driver's side of the yellow 2009 Chevrolet Camaro and opened the door, sliding into the seat while trying to conceal the exhaustion he was feeling. The door shut by itself as he pulled his legs in and buckled his seatbelt.

"_Falling asleep on the job? Cal-,_"squawked the radio. Sam rubbed his temples with his thumbs, his relationship problems filling his skull. He twisted the keys in the ignition, where they had been hanging even before he got in. You didn't need to worry about carjackers when your car was capable of self-defense. Sam once come back to find a smear of blood on one of the doors which had been rather distressing, but Bumblebee, his ever-trusty alien guardian, had sworn that he had only broken the thief's nose. Sam had gotten Mikaela to clean the blood off and neither he nor Bee had ever mentioned the incident again.

The engine started and revved by itself. Sam rested his head on the wheel.

"Oh, I'm fine Bee. I've just got a lot on my plate right now. Can you drive? I need to get back and freshen up before my date," he said.

"_Girls take a lotta work-_"the radio answered. The Camaro pulled out of its parking place and began to exit the garage under its own control.

"And you would know because…?" Sam said tiredly. Then a thought struck him, tagged onto a question he'd always been too embarrassed to ask his Autobot friend.

"Actually Bee, I've always meant to ask…are there really…y'know, female Autobots? Or is the whole gender thing just a matter of choice?" he said. He felt his face turn a very light shade of red. The radio crackled again.

"_Well, you see dear, when a man and woman love each other very much, they-_"his friend started to say. Sam quickly sat up straight.

"I think I get the idea Bee." He said hurriedly. He was no stranger to sex, but discussing said activity in relation to a species of giant alien robots was just too weird, even for him. He switched to a less delicate portion of his line of questioning.

"Does that mean you've got family? I mean, I never really thought about it that much, but-"he started to inquire. The radio cut him off.  
"_I'm an orphan, sir.-War took everything I loved-_" Said a little boy's voice over the speakers, followed by the tone of a gruff military recruit. Sam was shocked.

"What, really? No one at all?" he said.

"_Nada, nothing, not a one-_"the Autobot replied. Sam was dazed. "Why didn't you ever say?" he said, confused.

"_-don't need pity._" The radio replied.

"Do you have anyone left that you care about…y'know in a…I don't know, 'meaningful' way or something?" Sam said, trying to find lighter ground to tread on. There was a pause, then the radio answered. It didn't say anything, but it played out a slow, soft tune that sounded slightly like wind-chimes blowing about in a breeze. It took Sam a moment to make the connection but when he did, it was staggering.

"You know, she really doesn't strike me as a very stable personality." He replied. The radio played back a recording of his voice.

"_And you would know because…?_" it replied snidely. Sam felt bad about his comment, but Arcee, before becoming Mikaela's guardian, just as Bumblebee was his, hadn't struck him as being 'all there'. Of course she had been killed and then brought back to life in three separate bodies by the Decepticon version of a Frankenstein before making it to Earth, but there seemed to be more to it. Sam wasn't an expert on alien body language, but she seemed to carry a lot of guilt on her shoulders along with her trauma.

Since they had first met, she had been blown up, then restored again, this time in a single body, and had witnessed the death of more than a few of her close Autobot friends when Barricade had kidnapped Mikaela in an attempt to get to Sam a few years earlier. Arcee had disobeyed orders and gone after the Decepticon herself, beaten him severely, then driven him off and rescued Mikaela, earning her the job of being Mikaela's guardian.

The Autobot had become more approachable (if that was the right word) as she watched over her human charge, but Sam had never been able to figure out how or why. Anyone who had experienced as much loss and pain as Arcee should have been insane, but now he was beginning to see that maybe the reason as to why she didn't seem to be suffering from so much inner torment any more was not an event, but a person.

"Does she have any family?" Sam asked nonchalantly. The radio buzzed with static while its dials moved by themselves, and then answered.

"_Oh, I could name a few._" It chuckled.

A/N: Read review, don't be harsh. It's my first real story on here…


	4. Part I Chapter 2: New World Order

Chapter 2: New World Order

On the other side of the planet, somewhere in a region of the Indian Ocean branded off limits to all but a select few and blacked out from the readings of all human satellites, on the uppermost level of one of the spires of Atlantis, city of the Ancients, Colonel John Sheppard official head of the Atlantis Expedition,…was eating a lemon. He had picked up a habit of eating the fruit like other people ate oranges (with quite a bit of sugar to mitigate the acidic taste) as a means of controlling (and annoying) his friend Rodney McKay when his arrogance got out of hand. He had carefully peeled it with a small Swiss Army Knife and was now eating it slice by slice while he pondered his recent life and stared out over the railings at the city below and the ocean beyond.

Life had been mercifully quiet these past few weeks, unlike the years that had preceded it. Since its formation, work had been pretty thick when it came to saving the galaxy for the Galactic Defense Alliance (its original name, 'the Compound Alliance', just hadn't stuck). In between the long periods of nothing-to-do and the endless low-level changes to the status quo, there had been revelations, resurrections, reunions and revolutions, and that was just the 'R's. Just keeping it all straight was a task in itself.

Right now, John was wondering how to put it all in perspective. Maybe someday, when the time came for the history books to be written, it would all make sense. But right now, it was all a mess in his head. Behind him, the door to the transporter he had used to get here hissed open. This was followed by a string of curses in an all-too-familiar voice.

"Pressed the wrong button again?" he said without looking around. Sheppard fancied he could hear Lennox grinding his teeth as he turned to face his superior.

"Y'know, it fs not my fault all the labels are written in a language that looks like it was invented by someone with a Tetris fetish," he hissed out angrily. Sheppard just shrugged.

"You could try learning to read the stuff, you know." He answered before taking another bite of his lemon. He turned around to face the closet-like alcove where Lennox had now slid down into a sitting position with his hand on his forehead. The man sighed in resignation.

"I swore I'd never take another foreign language class after high school. Besides, couldn't Jackson just make a booklet of important phrases?" he muttered in response.

"I asked him about that once. He laughed for about ten minutes afterwards." Sheppard replied. Lennox rolled his eyes.

"What are you doing up here anyway?" he said irritably, "Jackson called for you ten minutes ago.".

"So, that's where were you actually headed?" John replied cheerily. Lennox rose to his feet, a tired look in his eyes. He had never been able to get the hang of traversing Atlantis by transporter, and almost every time he had tried, it had taken him four or five tries to find the right exit. The man was an excellent soldier, but when it came to reading Ancient, Sgt. Siler from the SGC was probably better than him.

"You know, sir, if I didn't know better, I'd think you were trying to avoid this meeting." He said impatiently. John put on his best mock-affronted look.

"Whatever gave you that idea?" he said haughtily. Lennox glared.

"We scheduled this extradition two weeks ago. We've been preparing for it for even longer. The only reason you'd be here instead of there right now is if you didn't want to be." The Major replied angrily.

John prepared to give another snarky retort, saw the man's expression and shut his mouth. With an air of resignation, he walked over to the closet-sized alcove of the transporter station and reached towards the control screen situated on its inside wall.

Before he could press the button over the control tower, his ear-radio chirped, signaling that someone was paging him. He changed the trajectory of his hand in midflight, an event some would pay money to see, and reached instead for the hearing-aid sized device, flicking the tiny on-switch to receive the incoming message. As he did, he rolled his eyes at Lennox, who nodded in understanding.

"This had better be important." He said as soon as the channel was open.

"Sheppard, I need you in the control room. The League ambassador is about to beam down and you were supposed to be here ten minutes ago to greet him." said a voice that had become as familiar to John as that of his friend Rodney. It was the voice of Dr. Daniel Jackson.

The man had been assigned to the city as chief liaison by the I.O.A. several years back after SG-1 had been virtually dissolved, where he had helped bridge the divide between the Autobots and the I.O.A., as well as keeping everything that was going on straight when John didn't have a hope in hell of doing the same.

When they had first met he hadn't been sure what to make of the man. All he knew from his brief prior encounters was that he was Rodney's counter-part in the field of understanding other cultures and archeology. Since then he had come to respect him, especially since on more than one occasion, his skill as a diplomat had saved Earth from annihilation due to the occasional misunderstanding.

"Thank you for the reminder, I'll be right there." He said, pouring as much irony into his voice as he could in order to be heard and understood over the radio. He stepped into the transporter with Lennox,

"What is it?" his subordinate asked as John tapped the button for the central tower, causing the doors to slide shut. As the flash of white light caused by the sudden matter-to-energy-to-matter process the transporter used to 'teleport' its occupants enveloped the pair then receded, John sighed with resignation.

"I'm late." He said, his disinterest made excessively clear via his body language.

"No, really?" Lennox said sarcastically. John rolled his eyes as they stepped out of the booth and into the main tower control room, lit with a combination of the fluorescent lights and the shine of the early morning sun. John grimaced.

"Look, it's not that I don't like a little bit of diplomacy with an ambassador from a spacey version of the U.N. at nine in the morning, but I really don't see the point. Jackson's going to do all the talking. I'm just going to stand there and watch the whole thing go down. It's not like I'm vital to the process." He said in annoyance. As they made their way past the various large trapezoidal consoles that filled the control room, each diligently manned by a trained operator and their coffee mugs, John continued to gripe.

"I mean, Rodney doesn't have to be here. Neither do Teyla or Ronon. Only me. Why me? I feel like some sort of decoration." He said irritably. Lennox snorted with a barely contained laugh.

"Rodney's on leave with Keller. He has been for two weeks. Ronon is still recovering from that raid you conducted on one of the Lucian Alliance's R&D facilities, and Teyla is lobbying the League to get her people membership and representation. She has been ever since we found out Michael was alive and in charge of the Lucian Alliance six months ago." He said, still trying to repress a chuckle.

"Don't remind me." Sheppard said, and he shuddered on the inside at the memory of seeing that pale face appear on the view-screens of the Daedalus, a face he had personally helped throw off the central spire of Atlantis…or so he had believed. The revelation that he had not killed Michael himself, but rather a deluded clone of the Hybrid had shocked Sheppard to his core. Now the being that had once been the greatest known threat to the Pegasus Galaxy was loose in the Milky Way and in command of his own empire. It was only a mercy that he hadn't started a galaxy-wide war…yet.

The thought of Michael seeking dominion of the Milky Way was a terrible one, but unfortunately entirely within the realm of possibility. The Hybrid was a power-hungry perverted genius, a master of genetics, chemistry and biology. More recently, word was he had taken up cybernetics and robotics as well. His interest in the Autobots had been one of the reasons for the formation of the G.D.A..

Three weeks ago, he and Ronon and Rodney had broken out a bunch of Autobot prisoners from the facility where Michael was conducting most of his research on the uses of Energon, the 'life-blood' (whatever that meant) of the Transformer species. It was one of many such bases he and his team had blown up in their crusade against the Hybrid-controlled Alliance, and with the help of the _General Hammond_, now under the command of Colonel Cameron Mitchell, they had destroyed that one too, though not before a prototype Ultra-Wraith, a thing that had looked like something from H.R. Giger's nightmares, had savagely attacked them after being released from the holding pens under the base where presumably similar or even worse genetic abominations had been kept. One swipe from the beast's tail had shattered four of Ronon's ribs and made Rodney twist his ankle as he ducked to avoid the scything appendage.

It had taken a full five direct hits from the Autobot air support they had brought along to cripple the thing, and even then, Sheppard could've sworn it was still trying to get up. Afterwards, he and a hobbling Rodney had done their best to tow Ronon back to the Stargate, while in the distance the _Hammond_ rained down fire and destruction on the complex from orbit. The encounter had gone down in his memory as one of the most terrifying events in his career.

As they descended the steps leading down from the control room to the main gate-room, Sheppard examined the new ambassador from the League of Unified Worlds (a name whose acronymical form General O'Neill had yet to finish finding ways of mocking), the first-ever organized, multi-galactic federation of governments, founded by survivors of the Tollana Massacre and the Tok'ra, he found he recognized him from his mission files of SG-1's adventures: Jonas Quinn, the team's replacement for Daniel Jackson after he had ascended the first time. Now he was the ambassador of the L.U.W. to Earth? That was quite a career change, but then, the man had been a physicist when he had first joined the SGC before becoming an archeologist during his tenure and then a geologist upon his return to his homeworld, so politics wasn't an incredible leap…mostly. Standing next to him was Dr. Jackson himself, giving John a 'where-the-hell-were-you' look.

"Colonel, how nice of you to finally join us. This is Ambassador Quinn, whom I'm sure you've heard of." He said, scathing sarcasm filling the first sentence. The ambassador didn't seem to notice or if he did, hid his response. He didn't look irritated in the least, but then, he was a politician. He stretched out his hand with a beneficent smile on his face. John took it and felt the firm handshake of an honest man.

This immediately made him suspicious, since he only ever put honesty and politics together when thinking of Mr. Woolsey and, perhaps, President Hayes. Experience had long ago taught him that governments often dealt in matters of convenience more than they did matters of conscience. Still, the man had served with SG-1 for two years and that had to count for something. He decided to give him the benefit of the doubt.

"It's nice to finally meet you Colonel. I've heard much about your exploits, particularly in opposing the Lucian Alliance. I have to say I am extremely impressed." The well-dressed man said. John put on his best politically-correct smile.  
"Thanks. We've done our best to try and curb their activities where we find them, but they're like roaches. They just keep coming back." He said. Jonas frowned.

"Well I hope that a permanent solution can be found soon." He said diplomatically. He turned back to Daniel.

"Dr. Jackson has filled out the release forms signed by the majority of League representatives prior to my arrival and we are ready to receive payment for the transfer." He said. Daniel nodded and beckoned a hovering S.F. waiting nearby who was holding a large plastic storage case about the size of your average dinner plate. He stepped forward and proffered the case to Jonas, who moved forward, undid the plastic clasps and opened it. Inside, set in a neat cavity carved into the grey packing foam of the box's interior was a single hard-drive, grey and silver. Jonas then closed the box and buckled the plastic clasps back into place.

"As promised, everything we know about the Autobots, including Dr. McKay's research into their technology and…anatomy, as well as what little we've been able to glean of their culture." Daniel said as Jonas relieved the soldier of his burden and stepped back. Then he raised his wrist and, still holding the box by its suitcase-like handle, he pressed several buttons on the wristwatch sized device he had been wearing.

"As per our agreement, we shall now release the prisoner into your custody. He should be beaming down now." The ambassador stated. Daniel looked at Lennox, who quickly tapped his ear-radio in response.

"This is Lennox to Reception Site Team, is the prisoner in custody?" he said. After a few seconds, an answer in a deep, powerful voice came back over the radio in response to his question.

"We've got the Decepticon punk locked down. He's not going anywhere." said Ironhide, Chief Weapons Officer of the Autobots present on Earth. Lennox nodded to Jackson.

"The prisoner is in our custody." He stated. The ambassador smiled cheerily.

"Well it looks like that's all. I'm going to be staying for a few days since the L.U.W. wants me to try and open formal relations with the Autobots. If someone could show me to where I'll be staying…" he said, looking directly at John. John, in turn, looked at the SF who had been holding the hard drive.

"Airman, kindly escort Ambassador Quinn to the guest quarters we had set aside?" he said in the same cheery voice Jonas had used. The man saluted briefly.

"Yes, sir. This way, Ambassador." The man said. Together, the pair exited the gate room at a brisk walk. After a full thirty seconds of silence, John said quietly: "I still feel like a decoration.". Lennox made a choking sound which suspiciously resembled repressed laughter. Daniel's eyes rolled so far upwards they were nearly showing all whites.

One mile away, on tarmac of Diego-Garcia's runway, was a battered and beaten looking black and white Cybertronian. He was sitting cross-legged and his hands were secured behind his back by two huge glowing red handcuffs which crackled with tiny arcs of slow-moving electricity. He was surrounded on all sides by armed and fully-kitted G.D.A. soldiers and about twenty Autobots, all of whom had their guns aimed at him. On the dented and pitted metal frame that made up his upper arm was a quote, painted on in grey and white. It was nearly unreadable due to the scuffing and scratches that covered it, but close examination would reveal to any careful observer what it really said.

With a deliberate and dramatic slowness, Barricade drew his gaze up to look at the Autobot now looming over him.

"Welcome back to Earth, Decepticon scum." Ironhide said. The Decepticon began to make a harsh, hacking, repetitive wheeze that Ironhide eventually realized was laughter.

"Ironhide, my old mentor. So nice to see you again. A lot's changed since I left last time, but time is something I do not have. I-"he began to say, until Ironhide shot him with the large Paralysis Cannon the Autobot inventor Steeljaw had created for this express purpose by combining Wraith stunner technology with his own. Blue static washed across the Decepticon's body and he fell backwards, his crossed legs coming uncrossed as he jittered from the blast.

"N-n-no, please, I have-have t-t-t-to war-"he tried to say before the energies of the gun's blast forced his body into a temporary stasis lock. Ironhide grunted.

"You'll have plenty of time to gibber once we get you into a nice cozy cell five-hundred feet below sea level." He growled. He turned his gaze back to the crowd, which parted to let Ratchet, the chief Autobot Medical Officer pass. He stood over the body and extended his bright red Diagnostic Laser, which he proceeded to run over the prone Decepticon's body. Once finished, he turned his gaze to Ironhide.

"He's out, just as it should be. He won't come back online any time soon. I'd wager forty-eight hours give or take a few minutes." The green-skinned Autobot stated. Ironhide turned to Master Sergeant Robert Epps, who had been standing at his rear left.

"The prisoner is ready for transport to Area 51, Sergeant. " Ironhide stated. Together, they looked down at the 'unconscious' Decepticon, Ironhide with disgust, Epps with curiosity.  
"Guy looks like he's been through hell. Wonder what he did to get this banged-up?" the human Sergeant Major said.

Ironhide snorted and replied darkly, "We'll find out soon, one way or another.".

A/N: I've been informed by a reliable source that my previous version of Chapter 1 was too long. I have to say after much consideration that this was true. As such, I have divided the aforesaid chapter into 2 chapters. Please don't hate me for it. I'm just trying to make it easier to read.


	5. Part I Chapter 3: What Lies Below

Chapter 3: What Lies Below

Mars. Until about three years ago, it had been overlooked by the galactic community. Even the G.D.A. who had the means and resources to investigate their closest planetary neighbor, never bothered to do so. It wasn't a very thoughtless decision. After all, the stars teemed with more lucrative and interesting ventures than investigating a dusty rock. But then several ships full of Ex-Decepticons and formerly imprisoned Autobots had arrived to supplement the constantly growing Cybertronian population of Earth. And it hadn't stopped there either. Shortly afterwards, the Ark, the damaged, bleeding Autobot mothership that had gone unheard from for centuries arrived at the edge of the solar system with nowhere to land, carrying what little remained of the population of Cybertron that wasn't Decepticons.

By this point, every Autobot who wasn't dead, M.I.A. or totally incapacitated had come to Earth. And Prime himself, the proud and determined Autobot leader, was already out scouring the stars for the injured and imprisoned stragglers. It quickly became clear to those in charge that there was simply not enough room on Earth for two sentient races. For one thing, there was no area big enough or secret enough to conceal their presence forever. So they did what politicians do best: they improvised.

Finally, after a month of political infighting, Mars was chosen as the perfect contingency, a perfect place to house the wayward Cybertronians. It kept them close enough to Earth so that they didn't feel unwanted, but provided a vast and cheap area to house them. They quickly mapped out large cave systems and set about expanding them with the help of the Autobots.

Today, on the day of Barricade's return, there were over thirty-five thousand Autobots living beneath the surface of Mars, not counting the Decepticon Defectors, who totaled about a thousand. The entirety of the surviving population of Cybertron still devoted to freedom now lived and worked and struggled in the dark beneath the Red Planet. It wasn't pretty, but it was a beginning.

For Elita One, it was both of these. She had abandoned her former rank of Supreme Admiral, given that the last dregs of the Autobot space forces were scattered across the solar system or slowly being disassembled to build their new home. Now she was a General, like Ironhide, trying to make her way in this new world and to direct her people to a better future.

It wasn't Cybertron. It could never be Cybertron. For one thing it was a great deal smaller than her mechanical birthplace. The huge and complex, ever-shifting superstructure of the planet, built on a core of molten rock and a few fragments of crust, could never be replicated. It was hard to believe that it was really gone. When she had left it, it had been war-ravaged certainly, but there was still the hope provided by the quest for the Allspark. Then three years ago the Ark had arrived and revealed that the planet had been annihilated by its expanding sun.

They should have seen it coming, but the war had occupied everything. They had forgotten their history, their culture, their religion, if they had ever had one. They were a people without purpose. Only Optimus, and his ideals, his strong sense of duty and his vision of a new Cybertron, kept the war-weary and battered population in line. They believed in him. They thought he had a plan. She wished she knew what it was.

But deep down, she could tell that he was standing on the edge. He didn't know where to turn. She had been with him for a long time and it was clear to her that he saw the humans and their civilization flourishing while the last remnants of Cybertron tried desperately just to survive. They were given help, of course, but they had fallen so far…would they ever be able to reclaim what they had once been?

She looked up from her reverie. Today, she was overseeing the rebuilding effort. It wasn't something a General should be doing, but she, like Optimus, believed that leaders should be among their people, not holed up with other leaders, making decisions in private. She cared for her people. She wanted the best for them, just like Prime. Which was why, today, she was overseeing the creation of a new cavern, slated for use as a medical area for any Autobots that might be injured in their daily activities.

Slowly she stood from where she had been sitting by the back of the cave on a particularly large rock. She stood about fifty feet tall, rivaling Prime himself in stature, which gave her a towering presence that made it hard for many humans to speak to her. Unlike Optimus of course, she possessed a feminine design, unmistakable in its intent of proclaiming gender difference even for something that most humans would consider nothing more than a machine. All in all, it made her a bit unnerving to be around, at least for those who didn't know her.

The site had two humans in E.V.A. gear overseeing it with her, ones she hadn't met before. They stood by on scaffolds next to her while the massive Digger, a gigantic earth-boring machine whose bits had been salvaged from the Ark ground away. It was a massive thing that resembled a nightmare made of teeth crossed with an industrial mining machine like those on Earth, driven by a single Cybertronian on a platform at its rear. So far the machine had cored eighty feet into the solid rock of the cavern wall. There were about ten other Cybertronians there, all operating various bits of geological equipment or shoring up the walls. The humans were simply there to oversee the process

The noise was practically nonexistent. The caves weren't pressurized. After all Mars had little enough air to begin with, most of it carbon dioxide. The Autobots didn't need air either. They got along fine with personal communication, which to a human would be the equivalent of telepathy…very limited, unremarkable telepathy. It didn't go much farther than allowing communication without speech. The humans talked to the Autobots in the same fashion with their radios, which were attuned to the bandwidth the Autobots used.

After five minutes of further observation, one of the humans spoke to her. He was understandably nervous, talking a giant techno-organic alien with pink and white highlights that could turn into an assault jet at will (an act that ninety percent of humans wouldn't even attempt for fear of inadvertently provoking a response warranting a squashing), but he seemed less intimidated that interested, which was good. But this man, while clearly not entirely comfortable, was not overly-intimidated either.

"Um…I hate to disturb you, but I was just wondering, how exactly did a digging device end up on the Ark? I mean it's supposed to be a battleship, right?" he said. She turned her head and studied him briefly in the floodlights being used to light the cavern. His nametag read 'Marshall'.

"_The Ark wasn't always a warship. It was supposed to be our first colony ship. It would have been our greatest endeavor. At the time it was built there was still peace, but when it neared completion factions had already formed. In the end, it was never fully converted to a ship of war. Much of the equipment that would have been used to seed a new world was left onboard._" She replied.

"And, uh...how does the guy over there know how to work it? Or does he just have to observe it?" the man asked, pointing at the Digger's operator. Elita allowed herself a small smile.

"_Bulkhead was chief of mining operations back on Cybertron. He directed the digging of geothermal wells to allow power plant construction. He's very good at it._" She said.

"_Damn right I am!_" the Autobot quipped. He had a voice like that of a gruff, veteran oil driller and the demeanor of one too. Many Autobots had adapted to humans by taking on such personality quirks.

"_Hey 'Lita, remember back when we were fightin' with Subshock on Grondia and he chased us into the ruins of the city sewers? There's another two hours I wouldn't want to repeat!_" the big green Autobot chuckled. Elita didn't exactly laugh. It had been an experience that even the lens presented by retrospective couldn't totally blur into a happy memory.

"Why? What happened?" Marshall asked.

"_It wasn't a very fair fight. Bulkhead had punched him so hard that his optics were damaged. We lured him into a weak intersection and dropped the street above on him._" She said.

"And that took two hours?" the human overseer asked in confusion.

"_No, that took 'bout twenty minutes. The next 'hundred were spent sloggin' through centuries-old water lookin' for a way out. By the time we found one, battle was half-over._" Bulkhead said, snickering, "_Still, Breakdown said the look on Blitzwing's face when you punched your way up through the street was priceless. He thought Subshock had us beat. And then you came out and tore that murder-happy split-spark a new exhaust vent._". He sighed over the channel in grim, but satisfied hindsight.

"_That was pretty good d-_" he started to say, then was cut off when even in the near-airless atmosphere of the cave, there came the sound of the drill's ending squealing on something.

The drill was tipped by three massive rotating grinders that resembled circular saws, arranged in a triangle. They spun together and turned granite into gravel. Whatever they had hit had other ideas though and was putting up an irresistible fight.

"_Bulkhead! Back up and shut down the Digger. It seems we've found something._" She said. She quickly donned the air of authority that brooked no disobedience and which had saved the lives of many under her command by overriding their fear and driving them to obey. The other Autobots in the chamber quickly turned to her for orders.

"_Stand together and get some light on whatever it is. It's not supposed to be here, but we're going to find out what it is before we do anything. Bulkhead, come with me._" She said. He nodded and jumped down from the control platform of the digger as she turned to the humans.

"_I suggest you notify your superior. This could be nothing more than a barrier to our construction but it might not. Once you have, I suggest you come with me. You should probably be there to see it, whatever 'it' is._" She said. She knew she had no power over the humans. They weren't part of her command structure. But all the humans she met had great respect for her people, bar a few inconsiderate types, and this one appeared to see the wisdom of her advice. He was silent for about two minutes and fifty seconds while he informed his superiors and obtained permission to accompany her, then re-opened his channel to the Autobots.

"Okay, I'm ready. I have clearance. But they said nothing was supposed to be down here. The geological surveys said that this area was free of anything that might be tough enough to block the drill." He said, making his way over to the edge of the scaffolding and jumping the twenty feet down to the ground, trusting in the planet's lower gravity to protect him. He was not disappointed and Elita nodded in concern.

"_They did. I was present when the expansion plans were made. But clearly they were wrong._" She replied.

Then, with Marshall following her, she made her way over to Bulkhead, who was standing patiently by the machine he had just been operating. He had retracted it from the hole just enough to leave space for Elita and himself to slip between the drill and the rock wall. As they entered the dark shadow of the tunnel they activated their personal lights, flooding the tube with brilliant white illumination. Their lights showed a rock tunnel eighty-six feet long stretching off into the distance…and at its end, a very different color of rock. The tunnel around them had the color of all of Mars, a dull, dried-blood red of sandstone layered with iron oxide. The rock revealed by the infringing drill was tan, like baked clay almost. But that wasn't the most important part. What was important was enormous door that had been carved into the rock, an edifice that stretched up beyond the roof of the tunnel which cut it off at about sixty feet. And on the door were two figures. One was a kneeling, androgynous human. The other…was a Cybertronian, in the same position, opposite the human.

"_What the hell?_" the overseen said in a hushed voice. Elita couldn't quite frame her thoughts, but if she had been able to, she would have probably said something similar. Bulkhead was enthused already. He strode up to it and examined it carefully.

"_It's not even scratched._" He said in awe. He was right. Despite the deceiving color of the portal and its surrounding rock, which contrasted with its look, which was of serious stonework and cathedral-esque architecture, it was totally unblemished by its encounter with the drill. Bulkhead shined his lamps back down the passage at the drill.

"_It's broken twelve teeth on the central grinders._" He observed.

"What's it doing here? There's not supposed to be anything on this planet besides us!" Marshall squeaked. Elita opened a channel to the Autobot command center where Optimus was located several thousand feet of solid rock overhead.

"_Elita? What is it? We've been overseeing the extradition of Barricade. I didn't expect to-_" the Autobot leader began, but she cut him off, something she rarely did.

"_Optimus, I need the humans to send their best archeologists and if we have any Autobots with similar skills send them too._"

"_What?_" he answered. It wasn't like Optimus to get confused, but in this case she wasn't giving him a choice.

"_We've made a discovery._" She said.

A/N: Hey there, sorry for the magna-uber –super delay, but my life is very busy and my writing skills have gone rusty in between. I promise that this story is not abandoned. Nor will it ever be. I just have a lot to focus on. So thanks for reading this and being a loyal fan. BTW, a scene from my story, Stargate: Those Left Behind is referenced here which has not yet been written. Consider it a teaser, not a spoiler.


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